ArticleRNA (New York, N.Y.)2002
Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus.
Article in RNA (New York, N.Y.), 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed.
- The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- TheJournal of virology · 2022Article
- The global and local distribution of RNA structure throughout the SARS-CoV-2 genome.Journal of virology · 2021Article
- Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms.Molecular cell · 2021Article
- A Novel Cis-Acting RNA Structural Element Embedded in the Core Coding Region of the Hepatitis C Virus Genome Directs Internal Translation Initiation of the Overlapping Core+1 ORF.International journal of molecular sciences · 2020Article
- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms.bioRxiv : the preprint server for biology · 2020Article
- The Role of the RNA-RNA Interactome in the Hepatitis C Virus Life Cycle.International journal of molecular sciences · 2020Review
- Evolutionary Analyses of Base-Pairing Interactions in DNA and RNA Secondary Structures.Molecular biology and evolution · 2020Article
- Article
- Conserved structural RNA domains in regions coding for cleavage site motifs in hemagglutinin genes of influenza viruses.Virus evolution · 2019Article
- Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts.mSphere · 2019Article
- Potential of the Other Genetic Information Coded by the Viral RNA Genomes as Antiviral Target.Pharmaceuticals (Basel, Switzerland) · 2019Review
- The HCV genome domains 5BSL3.1 and 5BSL3.3 act as managers of translation.Scientific reports · 2018Article
- Functional RNA structures throughout the Hepatitis C Virus genome.Current opinion in virology · 2017Review
- The chaperone-like activity of the hepatitis C virus IRES and CRE elements regulates genome dimerization.Scientific reports · 2017Article
- Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.Frontiers in microbiology · 2017Review
- The 5BSL3.2 Functional RNA Domain Connects Distant Regions in the Hepatitis C Virus Genome.Frontiers in microbiology · 2017Review
- Links between Human LINE-1 Retrotransposons and Hepatitis Virus-Related Hepatocellular Carcinoma.Frontiers in chemistry · 2016Review
12 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The existence and functional importance of RNA secondary structure in the replication of positive-stranded RNA viruses is increasingly recognized. We applied several computational methods to detect RNA secondary structure in the coding region of hepatitis C virus (HCV), including thermodynamic prediction, calculation of free energy on folding, and a newly developed method to scan sequences for covariant sites and associated secondary structures using a parsimony-based algorithm. Each of the prediction methods provided evidence for complex RNA folding in the core- and NS5B-encoding regions of the genome. The positioning of covariant sites and associated predicted stem-loop structures coincided with thermodynamic predictions of RNA base pairing, and localized precisely in parts of the genome with marked suppression of variability at synonymous sites. Combined, there was evidence for a total of six evolutionarily conserved stem-loop structures in the NS5B-encoding region and two in the core gene. The virus most closely related to HCV, GB virus-B (GBV-B) also showed evidence for similar internal base pairing in its coding region, although predictions of secondary structures were limited by the absence of comparative sequence data for this virus. While the role(s) of stem-loops in the coding region of HCV and GBV-B are currently unknown, the structure predictions in this study could provide the starting point for functional investigations using recently developed self-replicating clones of HCV.
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